You can import a protein or peptide sequence into the Theoretical Protein/Peptide Manager from a FASTA file or manually enter it.

Open the Theoretical Protein/Peptide Manager

Procedure

  1. Open the Sequence Manager by selecting Sequence Manager on the BioPharma Finder home page.
  2. Select the Theoretical Protein/Peptide Manager tab.
  3. The Theoretical Protein/Peptide Manager page opens, showing the Sequence area and parameters.
  4. Theoretical Protein/Peptide Manager page
    Theoretical Protein/Peptide Manager page

Import a protein or peptide sequence from a FASTA file

Procedure

  1. In the Theoretical Protein/Peptide Manager, select Import Protein Sequence on the command bar and browse to the folder containing the FASTA file.
  2. The dialog box displays all of the FASTA files in the selected folder.
  3. The FASTA file must have the ".fasta" extension for the application to be able to find the file.
  4. Select a FASTA file to import and then select Open.
  5. The application displays the sequence information from the FASTA file in the Enter Peptide or Protein Sequence box, overwriting any previous content in this box.
  6. You can import FASTA files of 1 MB or less.
  7. If a FASTA file contains invalid amino acids or an invalid format, an error message appears. If an error message appears during the import operation, open the FASTA file in a text editor such as Notepad and verify the format of each chain.

Manually create a protein or peptide sequence

Procedure

  1. In the Sequence area of the Theoretical Protein/Peptide Manager, type the protein or peptide sequence in the Enter Peptide or Protein Sequence box.

  2. NOTE

    You cannot specify both proteins and peptides at the same time; however, you can enter them in two separate sessions.

  3. When inputting protein sequence information in the Enter Peptide or Protein Sequence box, you must:
  4. Use the approved amino acid alphabet.
  5. See Amino acid letter codes.
  6. Begin each chain with a single-line description.
  7. Use a greater-than (>) sign at the start of this line to distinguish the chain description from the sequence data.
  8. Use no space between the > and the first letter of the identifier in the description.
  9. Follow the description with lines of sequence data in the form of amino acid single-letter codes.
  10. A chain ends when another line starting with > appears, indicating the start of another chain.
  11. When inputting peptide sequence information in the Enter Peptide or Protein Sequence box, you must:
  12. Use the approved amino acid alphabet.
  13. See Amino acid letter codes.
  14. Use a contiguous sequence of characters to define each peptide.
  15. Enter multiple peptides on separate lines.
  16. If you want to perform digestion on the protein, select the Perform Digestion checkbox at the top right of the Sequence area.
  17. For more information on digestion parameters for theoretical proteins, see Specify digestion parameters.
  18. To perform the theoretical experiment without changing the default Digestion Parameters (optional), Add/Edit Target m/z, or Add/Edit Modifications, select Process.
  19. The Results table displays the results of the theoretical experiment.
  20. See Results table parameters.
  21. Otherwise, you can edit the Digestion Parameters, Add/Edit Target m/z, or Add/Edit Modifications as needed.
  22. See the following topics:
  23. •Specify digestion parameters
  24. • Add/edit target m/z parameters
  25. •Add/edit modifications